Nanoparticles transported through highly confined porous media exhibit faster breakthrough than small molecule tracers. Despite important technological applications in advanced materials, human health, energy, and environment, the microscale mechanisms leading to early breakthrough have not been identified. Here, we measure dispersion of nanoparticles at the single-particle scale in regular arrays of nanoposts and show that for highly confined flows of dilute suspensions of nanoparticles the longitudinal and transverse velocities exhibit distinct scaling behaviors. The distributions of transverse particle velocities become narrower and more non-Gaussian when the particles are strongly confined. As a result, the transverse dispersion of highly confined nanoparticles at low Péclet numbers is significantly less important than longitudinal dispersion, leading to early breakthrough. This finding suggests a fundamental mechanism by which to control dispersion and thereby improve efficacy of nanoparticles applied for advanced polymer nanocomposites, drug delivery, hydrocarbon production, and environmental remediation.